library(Seurat)
library(ggpubr)
library(dplyr)
library(useful)
library(plyr)
library(RColorBrewer)
cd8_seurobj <- readRDS("scRCC_CancerCell_ReviewerResponse_CD8s_SeurObj.RDS")
head(cd8_seurobj@meta.data)
umap_cols <- c('#7FC97F','#5C86AB','#EB0A75', '#8B3B99')
DimPlot(cd8_seurobj, cols = umap_cols)
DefaultAssay(cd8_seurobj) <- "RNA"
Idents(cd8_seurobj) <- "patient"
p55 <- subset(cd8_seurobj, idents = c("p55"))
p55 <- FindVariableFeatures(p55, selection.method = "vst")
top10 <- head(VariableFeatures(p55), 10)
all.genes <- rownames(p55)
p55 <- ScaleData(p55, features = all.genes)
p55 <- RunPCA(p55, features = VariableFeatures(object = p55), npcs = 60)
ElbowPlot(p55,ndims = 50)
p55 <- RunUMAP(p55, dims = 1:30)
DimPlot(p55, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p55) <- "RNA"
p <- FeaturePlot(p55, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p55) <- "RNA"
p <- FeaturePlot(p55, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p55, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p55, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p55, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p55, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p55, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p55, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p55, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p55, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p55, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p55, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p55, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p55, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p55, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p55, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p55_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()
p915 <- subset(cd8_seurobj, idents = c("p915"))
p915 <- FindVariableFeatures(p915, selection.method = "vst")
top10 <- head(VariableFeatures(p915), 10)
all.genes <- rownames(p915)
p915 <- ScaleData(p915, features = all.genes)
p915 <- RunPCA(p915, features = VariableFeatures(object = p915), npcs = 60)
ElbowPlot(p915,ndims = 50)
p915 <- RunUMAP(p915, dims = 1:30)
DimPlot(p915, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p915) <- "RNA"
p <- FeaturePlot(p915, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p915) <- "RNA"
p <- FeaturePlot(p915, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p915, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p915, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p915, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p915, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p915, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p915, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p915, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p915, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p915, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p915, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p915, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p915, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p915, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p915, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p915_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()
p913 <- subset(cd8_seurobj, idents = c("p913"))
p913 <- FindVariableFeatures(p913, selection.method = "vst")
top10 <- head(VariableFeatures(p913), 10)
all.genes <- rownames(p913)
p913 <- ScaleData(p913, features = all.genes)
p913 <- RunPCA(p913, features = VariableFeatures(object = p913), npcs = 60)
ElbowPlot(p913,ndims = 50)
p913 <- RunUMAP(p913, dims = 1:30)
DimPlot(p913, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p913) <- "RNA"
p <- FeaturePlot(p913, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p913) <- "RNA"
p <- FeaturePlot(p913, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p913, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p913, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p913, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p913, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p913, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p913, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p913, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p913, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p913, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p913, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p913, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p913, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p913, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p913, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p913_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()
p906 <- subset(cd8_seurobj, idents = c("p906"))
p906 <- FindVariableFeatures(p906, selection.method = "vst")
top10 <- head(VariableFeatures(p906), 10)
all.genes <- rownames(p906)
p906 <- ScaleData(p906, features = all.genes)
p906 <- RunPCA(p906, features = VariableFeatures(object = p906), npcs = 60)
ElbowPlot(p906,ndims = 50)
p906 <- RunUMAP(p906, dims = 1:30)
DimPlot(p906, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p906) <- "RNA"
p <- FeaturePlot(p906, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p906) <- "RNA"
p <- FeaturePlot(p906, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p906, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p906, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p906, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p906, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p906, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p906, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p906, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p906, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p906, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p906, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p906, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p906, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p906, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p906, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p906_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()
p76 <- subset(cd8_seurobj, idents = c("p76"))
p76 <- FindVariableFeatures(p76, selection.method = "vst")
top10 <- head(VariableFeatures(p76), 10)
all.genes <- rownames(p76)
p76 <- ScaleData(p76, features = all.genes)
p76 <- RunPCA(p76, features = VariableFeatures(object = p76), npcs = 60)
ElbowPlot(p76,ndims = 50)
p76 <- RunUMAP(p76, dims = 1:30)
DimPlot(p76, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p76) <- "RNA"
p <- FeaturePlot(p76, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p76) <- "RNA"
p <- FeaturePlot(p76, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p76, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p76, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p76, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p76, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p76, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p76, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p76, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p76, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p76, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p76, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p76, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p76, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p76, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p76, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p76_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()
p90 <- subset(cd8_seurobj, idents = c("p90"))
p90 <- FindVariableFeatures(p90, selection.method = "vst")
top10 <- head(VariableFeatures(p90), 10)
all.genes <- rownames(p90)
p90 <- ScaleData(p90, features = all.genes)
p90 <- RunPCA(p90, features = VariableFeatures(object = p90), npcs = 60)
ElbowPlot(p90,ndims = 50)
p90 <- RunUMAP(p90, dims = 1:30)
DimPlot(p90, group.by = "FinalCellType", cols = umap_cols)
DefaultAssay(p90) <- "RNA"
p <- FeaturePlot(p90, c("CD3D","CD3E","TRAC","TRBC2","CD8A","CD8B","CD4","GZMB","PRF1"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
DefaultAssay(p90) <- "RNA"
p <- FeaturePlot(p90, c("PDCD1","HAVCR2","LAG3","TNFRSF9","ENTPD1","IL7R","STAT4","MX1","MKI67"), pt.size = 0.1, min.cutoff = 0, combine = F, order = F, cols = c("grey85","firebrick1"))
for(i in 1:length(p)) {
p[[i]] <- p[[i]] + NoLegend() + NoAxes()
}
cowplot::plot_grid(plotlist = p)
umap <- DimPlot(p90, group.by = "FinalCellType", cols = umap_cols, pt.size = 0.4) + NoLegend()
cd3d <- FeaturePlot(p90, c("CD3D"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd8b <- FeaturePlot(p90, c("CD8B"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd4 <- FeaturePlot(p90, c("CD4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
cd69 <- FeaturePlot(p90, c("CD69"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdcd1 <- FeaturePlot(p90, c("PDCD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
havcr2 <- FeaturePlot(p90, c("HAVCR2"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
lag3 <- FeaturePlot(p90, c("LAG3"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
tnfrsf9 <- FeaturePlot(p90, c("TNFRSF9"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
entpd1 <- FeaturePlot(p90, c("ENTPD1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
il7r <- FeaturePlot(p90, c("IL7R"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
stat4 <- FeaturePlot(p90, c("STAT4"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mx1 <- FeaturePlot(p90, c("MX1"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
mki67 <- FeaturePlot(p90, c("MKI67"), pt.size = 0.4, min.cutoff = 0, order = F, cols = c("grey85","firebrick1")) + NoLegend()
pdf("p90_RNA_UMAP_Integrated_ClusterMetadata.pdf", useDingbats = F, width = 15, height = 5)
ggarrange(umap, cd3d, cd8b, cd4, cd69, tnfrsf9, pdcd1, havcr2, lag3, entpd1, il7r, stat4, mx1, mki67, nrow = 2, ncol = 7)
dev.off()